Welcome to my small and fun codes, written during my initial learning period as part of coding practice. These codes can serve as quick analysis tools as these run directly from terminal like commands.
STATISTICS
If you are starting Molecular Dynamics career using GROMACS and do not use python yet, this code can perform some of the statistical analysis on gromacs generated xvg files.
Syntax of this code is similar to gromacs,
>> Statistics sub_command -f ... options
>> list of sub_commands are available like bootstrapped mean, binding time etc
>> like gromacs, it does not overwrite, instead backed up the files
>> in addition to gromacs, if sub_command has some alphabetical error, it also suggest the correct names.
Usage:
put this code in any of your BASH PATH and modify python path (first line in statistics.py)
just write statistics in terminal, it should print usage.
for any help, just like gromacs, write
>>> statistics sub_command -h
PAIR_MAKER
In Molecular Dynamics simulations of proteins, pairwise distances is one better way of estimating the distances between two structures like helices etc. In gromacs, this requires index group (ndx file) in a pairwise manner which could not be generated by gmx make_ndx.
pair_maker can take gromacs index file (.ndx) containing the input index groups and generate new index group (pairwise index group).
Uage:
put this script in BASH PATH and modify python path (first line)
just write pair_maker, it should print syntax
Calculator and panalyze
As a terminal lover, I don't like to open calculator or jupyter-notebook (favoured python environment) for some quick mathematical calculations while doing any analysis.
Calculator.py and panalyze.py scripts can do that, just put in BASH PATH and adjust the python paths.
Calculator : for simple and direct calculations, like mean, product, permutation etc
Syntax : for example calculating 10C3 (combinations of 3 out of 10),
>>> calculator combination 10 3
Panalyze : for complex calculations
Syntax:
>>> panalyze -q " mathematical expression in numpy (np) format "
RCSB
As a protein biophysicist, downloading PDB structures is frequent exercise.
RCSB website do provide downloading path, but rcsb.sh script do it in nicer-fun way with rotating and colorfull progress bar etc....
Syntax:
>>> rcsb id1 (pdb id to download) id2 (optional, saving name with/without path)